More than 1.2 million U.S. homeowners have managed to avoid foreclosure and stay in their homes thanks to the government’s loan modification program. Thousands more have modified loans directly through banks.

But even as foreclosure rates subside, homeowners "underwater" on their loans -- those who owe more than their home is worth -- maintain one common complaint: paperwork delays seem to start, and end, inside banks.

In Joliet, Rita Zorba says she always figured she’d live out her life in the home she owns. Her recent, self-described "nightmare" of trying to get a home loan modified made her wonder if that plan would change.

"I started thinking I’d have to handcuff myself inside the house," she said.

Zorba said her headaches began about a year ago when she started the loan modification process with Wells Fargo, which services the primary loan on her home. She was hoping to lower her monthly mortgage payments after becoming unemployed and falling behind on her payments. When Wells told her she qualified for a trial period of lower payments, Zorba said she thought relief was in sight.

But then two words Zorba had never heard threatened to upset the plan in place: "subordination agreement."

"It took a while to sink in to really, really understand because I'm a lay person, I'm not a banker," the Joliet homeowner said.

"A subordination agreement is where a first lienholder is going to request from a second lender to acknowledge that they're second in line; that they're behind the first lienholder. So if you have a first mortgage with Wells Fargo, Wells Fargo agreed to give you this amount of money in exchange for them being first in line in the event of your default to come and take the secured asset in this instance, your home."

In Rita Zorba’s case, it works like this: Wells Fargo services her primary loan, so it is in first position to get paid if bankruptcy should occur. Banco Popular services Zorba’s second loan on the home, so it is in second position to get paid.

But Lattas and other experts said a subordination agreement is not necessary in a loan modification case. Lattas said Wells Fargo is the only major bank that requires the document, and the process often adds delays and frustration to an already complicated process.

"I mean, what I would hope is that Wells Fargo really examine why they're making this requirement. Is it an internal requirement or is it something that their investors are requiring because no other major lender is requiring this and if it was so necessary, why wouldn't Chase, Bank of America, One West, be making the same requirements. They're not. Wells Fargo is the only one that's doing it," Lattas said.

When a Wells representative floated a dreaded word, Zorba says she knew she had to take action.

"They will take my house and they will foreclose. That's when I cried, and then I got mad," she said. "I felt like I was being pulled every which way and didn't know which way to turn."

In responding to questions about why Wells Fargo requires a document many experts say is unnecessary, a Wells Fargo spokesperson apologized for the inconvenience but said the agreement is required by the investor (in this case Fannie Mae), in order to assure its first lien position.

As for Banco Popular, after NBC5 Investigates asked why it wouldn’t sign the agreement which reflects its second position, a spokesperson responded with "good news." The bank reversed course and agreed to sign the document. Banco Popular also said it did not realize the request was for a modification, rather than a refinance. A spokeswoman also confirmed the requirement is an unusual one.

Zorba now has the loan modification she sought for more than a year. She remains puzzled why it had to be so complicated and adversarial, but is glad she kept up the fight.

"I want people to know what subordination means, how to go about it so that they don't give up hope, they have some tenacity to keep going and keep pushing and not give up. Because I know a lot of people who just gave up and they wouldn't do what I did," she said.

Both banks now say Zorba's modification is official: $47,000 of her principal is now deferred and her monthly payments have been lowered significantly.

Zorba said the most frustrating part of her journey was that many of the places to which she turned to help told her they could step in if she was in foreclosure. But getting the loan modification to avoid foreclosure, of course, was her intent.